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Yorodumi- PDB-3fhm: Crystal structure of the CBS-domain containing protein ATU1752 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fhm | ||||||
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Title | Crystal structure of the CBS-domain containing protein ATU1752 from Agrobacterium tumefaciens | ||||||
Components | uncharacterized protein ATU1752 | ||||||
Keywords | structural genomics / unknown function / NUCLEOTIDE-BINDING PROTEIN / CBS domain / prokaryotic / bound nucleotide / AMP / NADH / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Singer, A.U. / Xu, X. / Zhang, R. / Cui, H. / Kudritsdka, M. / Edwards, A.M. / Joachimiak, A. / Yakunin, A.F. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the CBS-domain containing protein ATU1752 from Agrobacterium tumefaciens Authors: Singer, A.U. / Brown, G. / Proudfoot, M. / Xu, X. / Dong, A. / Cui, H. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fhm.cif.gz | 118 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fhm.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 3fhm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/3fhm ftp://data.pdbj.org/pub/pdb/validation_reports/fh/3fhm | HTTPS FTP |
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-Related structure data
Related structure data | 3rc3S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Details | Dimer as represented by molecules B and C |
-Components
#1: Protein | Mass: 17595.943 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: not cleaved with TEV. Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Strain: C58 / Gene: AGR_C_3216, Atu1752 / Plasmid: p15TvLic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIPL / References: UniProt: A9CIP4 #2: Chemical | ChemComp-AMP / #3: Chemical | ChemComp-NAI / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.87 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Tris 8.0, 0.2 M LiSO4, 30% PEG 4K plus 0.015 mg/ml V8 protease. Cryoprotected with Paratone-N oil, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Jun 16, 2008 / Details: mirrors |
Radiation | Monochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30.37 Å / Num. all: 24264 / Num. obs: 19824 / % possible obs: 81.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 47.9 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.55 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 1.1 / Num. unique all: 143 / % possible all: 11.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: model of protein made from 3rc3 using MrBUMP Resolution: 2.7→30.37 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.905 / SU B: 27.186 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.855 / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.886 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→30.37 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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